Contacts of the strand formed by residues 24 - 29 (chain S) in PDB entry 1KYO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 24 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249L ARG 3.8 8.3 - - - +
250L LEU* 4.5 0.5 - - - -
251L ARG* 4.0 18.5 + - + +
300O PHE* 3.9 29.8 - - + -
301O VAL 3.6 4.0 - - - +
302O PHE* 3.8 15.9 - - + -
69R TYR 4.3 2.2 - - - +
72R ALA* 4.0 8.3 - - + -
73R TYR* 3.5 45.8 - - + +
76R ILE* 3.7 23.3 - - + -
21S GLN* 4.7 13.5 - - + +
22S LYS 3.3 8.4 - - - +
23S GLY* 1.3 78.8 - - - +
25S THR* 1.3 64.8 + - - +
26S SER 4.2 0.4 - - - +
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Residues in contact with THR 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L VAL* 4.0 5.8 - - + -
249L ARG 3.6 6.5 - - - +
250L LEU* 3.4 33.9 - - + +
299O LYS 3.6 1.6 - - - +
300O PHE* 3.5 1.6 - - - -
301O VAL* 2.9 43.1 + - - -
303O ASN* 5.0 1.2 + - - -
33P THR* 3.6 16.2 - - + +
23S GLY 4.2 6.2 + - - -
24S ILE* 1.3 76.0 + - - +
26S SER* 1.3 61.1 + - - +
27S TYR* 3.7 29.0 - - + +
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Residues in contact with SER 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247L GLU* 4.0 2.8 + - - +
248L VAL* 3.5 4.3 - - - +
249L ARG* 3.0 55.4 + - - +
298O ARG* 4.8 8.8 + - - +
299O LYS 3.3 7.4 - - - -
300O PHE* 3.5 35.5 - - - -
24S ILE 4.2 1.0 - - - -
25S THR* 1.3 73.5 - - - +
27S TYR* 1.3 64.7 + - - +
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Residues in contact with TYR 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L SER* 5.9 0.7 - - - -
166L THR* 5.5 2.9 - - - -
247L GLU* 3.3 8.1 - - - +
248L VAL* 3.7 25.4 - - + -
298O ARG* 3.7 3.1 - - - +
299O LYS 3.0 38.0 + - - +
301O VAL* 3.9 17.9 - - + +
32P SER 4.0 0.9 + - - -
33P THR* 2.7 47.8 + - - +
35P ARG 3.9 4.9 + - - -
36P THR* 3.9 21.3 - - + -
37P PRO* 3.7 38.6 - - + -
39P PHE* 3.9 11.5 - - + -
25S THR* 3.7 23.2 - - + +
26S SER* 1.3 76.7 - - - +
28S ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169L GLN* 5.4 0.2 - - - +
246L SER* 3.2 6.1 - - - -
247L GLU* 2.9 54.4 + - + +
444L TYR* 5.7 4.5 - - + -
294O GLY* 4.0 19.3 - - - +
297O THR 5.3 0.4 - - - -
298O ARG* 4.4 13.5 - - + +
39P PHE* 4.3 6.5 - - - -
27S TYR* 1.3 76.7 - - - +
29S VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169L GLN* 4.6 0.9 - - - +
244L LEU* 4.0 12.6 - - + -
245L GLY 3.2 12.6 - - - +
246L SER* 4.4 3.8 - - - -
444L TYR* 5.0 3.7 - - - -
294O GLY* 3.8 9.7 - - - -
297O THR* 4.9 4.6 + - - +
39P PHE* 3.8 39.8 - - + -
42P VAL* 6.0 1.3 - - + -
43P LEU* 3.7 26.7 - - + -
28S ALA* 1.3 82.7 - - - +
30S SER* 1.3 76.5 + - - +
31S PRO* 3.5 4.5 - - - +
33S ALA* 3.8 10.1 - - + -
34S GLN* 3.2 20.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il